bioinformatics
Biodiversity informatics
26-08-2010 10:23
Bioinformatics, or more
precise, biodiversity informatics, is an emerging
field in which much progress already has been made.
However, overarching scientific questions seem to be
absent and therefore major, guiding goals are
missing.
In a recent review, Townsend Peterson et al. (2010) have tried to bridge this gap by posing a number of Big Questions.
According to these authors, “biodiversity science in general can and should evolve from a purely descriptive cataloguing endeavour into a predictive, scientific exploration of space, time and form”. This seems only logical.
This figure presents a framework of biodiversity informatics data realms, showing potential cross-links between some of them that are currently unlinked.
Given this framework the following areas of analysis could become available.
1. Geography and ecology of past life.
This topic is part of global change biology and seems to be very important when we try to anticipate biotic responses to future environmental change and biodiversity loss. The interaction of intrinsic and extrinsic factors on species’ responses remains little known.
2. Biota-wide picture of diversification and interaction
Community ecology currently focuses on closely relatives or known mutualists. However, a broader perspective is needed, leading to a more integrative view of both biotic interactions and biological diversification. Phylogenetic frameworks, geographic distributions and species niche estimates are key elements. This could result in insights incorporating ecological dimensions and likely shifts in distribution during historic times.
3. Future (novel) communities
Palaeontological evidence shows that in the past communities existed differing from extant counterparts. The shifts in novel species assemblages due to changing climates and the introduction of alien species may need further developments in niche modelling, leading to environmental change scenarios and future distribution predictions.
4. Integrating phenotype and genotype
Linking rich biodiversity data sets on phenotypes and genotypes of individuals, populations and species could be integrated over space and visualized in various dimensions. This would provide a view on how phenotype and genotype interact with geography and ecology.
5. Synthetic conservation planning
Only recently, conservation planning involves prioritizing using multi-factor, multi-temporal scenarios, which have the potential of covering more of the true complexity. This could lead to a more synthetic and robust view of conservation and nature resources management.
Some the key next steps involve data integration across disparate databases, data quality assurance, detecting errors and avoiding pseudoreplication, and finally, dealing effectively with scale.
All this - and more details in the paper - provides a challenging outlook. Undoubtedly, biodiversity informatics will become Big in the (near) future. But for me the key question is: what is the taxon involved? Having seen various incidents where people loose sight of the organism at stake, and focus instead on methodological questions and techniques to be used. “It’s the taxon, stupid”; even if this involves a purely descriptive cataloguing endeavour...
Reference:
Townsend Peterson, A., Knapp, S., Guralnick, R., Soberon, J. & Holder, M.T., 2010. The big questions for biodiversity informatics. - Systematics and Biodiversity 8: 159-168.
In a recent review, Townsend Peterson et al. (2010) have tried to bridge this gap by posing a number of Big Questions.
According to these authors, “biodiversity science in general can and should evolve from a purely descriptive cataloguing endeavour into a predictive, scientific exploration of space, time and form”. This seems only logical.
This figure presents a framework of biodiversity informatics data realms, showing potential cross-links between some of them that are currently unlinked.
Given this framework the following areas of analysis could become available.
1. Geography and ecology of past life.
This topic is part of global change biology and seems to be very important when we try to anticipate biotic responses to future environmental change and biodiversity loss. The interaction of intrinsic and extrinsic factors on species’ responses remains little known.
2. Biota-wide picture of diversification and interaction
Community ecology currently focuses on closely relatives or known mutualists. However, a broader perspective is needed, leading to a more integrative view of both biotic interactions and biological diversification. Phylogenetic frameworks, geographic distributions and species niche estimates are key elements. This could result in insights incorporating ecological dimensions and likely shifts in distribution during historic times.
3. Future (novel) communities
Palaeontological evidence shows that in the past communities existed differing from extant counterparts. The shifts in novel species assemblages due to changing climates and the introduction of alien species may need further developments in niche modelling, leading to environmental change scenarios and future distribution predictions.
4. Integrating phenotype and genotype
Linking rich biodiversity data sets on phenotypes and genotypes of individuals, populations and species could be integrated over space and visualized in various dimensions. This would provide a view on how phenotype and genotype interact with geography and ecology.
5. Synthetic conservation planning
Only recently, conservation planning involves prioritizing using multi-factor, multi-temporal scenarios, which have the potential of covering more of the true complexity. This could lead to a more synthetic and robust view of conservation and nature resources management.
Some the key next steps involve data integration across disparate databases, data quality assurance, detecting errors and avoiding pseudoreplication, and finally, dealing effectively with scale.
All this - and more details in the paper - provides a challenging outlook. Undoubtedly, biodiversity informatics will become Big in the (near) future. But for me the key question is: what is the taxon involved? Having seen various incidents where people loose sight of the organism at stake, and focus instead on methodological questions and techniques to be used. “It’s the taxon, stupid”; even if this involves a purely descriptive cataloguing endeavour...
Reference:
Townsend Peterson, A., Knapp, S., Guralnick, R., Soberon, J. & Holder, M.T., 2010. The big questions for biodiversity informatics. - Systematics and Biodiversity 8: 159-168.
'Freeware'
06-01-2010 13:06
I’m not only a
supporter of open access to scientific publications,
but also to open standards and freeware (or at least
low-cost) software for academic uses. And, crucially,
cross-platform.
For taxonomists, building keys is essential. However, software packages are scarce and usually commercial.
Lucid is one of these commercial packages and is more and more in use. Although it may be arguably seen as a marketing trick to lure you, I don’t want to withhold from you that currently Lucid 3.3 may be grabbed here for free.
The latest version is 3.5 and of course has more features, but I think version 3.3 is still an offer not to be refused. No warranty or support, however, and only for personal use. You need to register first as a member of Lucidcentral.org.
For taxonomists, building keys is essential. However, software packages are scarce and usually commercial.
Lucid is one of these commercial packages and is more and more in use. Although it may be arguably seen as a marketing trick to lure you, I don’t want to withhold from you that currently Lucid 3.3 may be grabbed here for free.
The latest version is 3.5 and of course has more features, but I think version 3.3 is still an offer not to be refused. No warranty or support, however, and only for personal use. You need to register first as a member of Lucidcentral.org.